Depending on available skills, surgical treatment of endometriomas can be by laparotomy or laparoscopy to strip the cyst wall or drain and ablate the cyst wall [23]. The laparoscopic approach is known to result in a quicker recovery, shorter hospital stay and less postoperative pain when compared to laparotomy [24]. Ovarian cystectomy requires mobilisation of the ovary followed by a small incision away from the ovarian hilus with any suitable electro-diathermy instrument, the harmonic scalpel or laser. The incision is then extended with scissors and the correct plane between the cyst wall and ovarian tissue identified. If difficult to identify a dissection plane from the cut edges, this may be facilitated by a small bevelled cut with curved scissors into the cyst wall, away from the edge. The cyst is then carefully stripped and removed from the ovarian tissue by opposing (180°) traction. The bed of the cyst needs to be inspected for any bleeding and light bipolar diathermy is applied as required. Ablative surgery is performed with a small incision to aspirate the chocolate coloured material. The cyst is then opened and washed out and its wall destroyed with bipolar diathermy or laser vaporization. When confronted with a large endometrioma, a useful technique is to turn the cyst wall inside-out to facilitate ablation, following which the ovary is reverted by invagination. Others have advocated a stepwise technique for a very large cyst, which is opened and washed out, followed by 3 months of GnRH analogues before a second ablative operation is undertaken [25]. Although this method preserved ovarian reserve better than cystectomy, this study did not compare three-step with single-step methods and did not include pregnancy outcomes or economic analyses [25]. It is therefore doubtful whether this technique will be beneficial to infertile women.

A recent Cochrane review looked into the most effective ways of treating ovarian endometriomas, comparing cyst excision with drainage and electro-coagulation. Cystectomy resulted in a reduced recurrence rate (OR 0.41 CI 0.18–0.93), reduced requirement for further surgery (OR 0.21 CI 0.05–0.79), reduced pelvic pain (OR 0.1 CI 0.02–0.56) and a higher spontaneous pregnancy rate (OR 5.21 CI 2.04–13.29) [26]. However, there was insufficient data regarding pregnancy rates after COI and IUI [26]. Another Cochrane review analysed the efficacy of surgery for women with endometrioma prior to ART. There was no difference in clinical pregnancy rate in the expectant and surgical (cystectomy or aspiration) group, although women with a cystectomy had a decreased ovarian response [27]. The ESHRE guideline recommends a laparoscopic ovarian cystectomy for endometrioma ≥4 cm [28, 29]. This reduces the risk of infection and improves follicle access during egg collection and possible improves ovarian response [28, 29]. Another study looked at the different haemostatic techniques after laparoscopic excision of an endometrioma and the effect of ovarian reserve and IVF outcome. They did not find a difference in IVF outcome between women treated with bipolar electro-coagulation or ovarian suture for haemostasis [30]. Those haemostatic techniques were also investigated in a randomized controlled trial and no difference was seen between the two haemostatic approaches and pregnancy rate and time to conception [31]. However, women had a reduced ovarian reserve following ovarian cystectomy irrespective of the method of haemostasis [31].

Infertile women with endometriomas needing IVF treatment may present a dilemma, particularly with the prospects of extra costs of surgery and associated further delay before able to start fertility treatment. A systematic review from 2009 comparing surgical with no treatment of endometrioma in women undergoing IVF did not reveal a significant effect on pregnancy rates [32]. However, a more recent study showed that the presence of endometrioma affected the numbers of oocytes retrieved, although oocyte quality and clinical pregnancy rate were not found to differ from women without endometrioma [33]. The long protocol with GnRH down-regulation has been shown to be favourable in women with moderate to severe endometriosis by increasing clinical pregnancy rate [34].

At the time of egg collection, it is important to avoid puncturing the endometrioma as the cyst fluid has adverse effects on the gametes. If the endometrioma is accidentally punctured, the needle needs to be retrieved and flushed with culture media or saline. Furthermore, intra-operative prophylactic antibiotics are recommended for all women with inadvertent puncture of endometrioma in order to reduce the risk of pelvic infection.